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Not AvailableBegomoviruses infecting legumes (family Geminiviridae) pose a serious threat to the productivity of grain legumes in general and soybean in particular. In this study, replication initiator protein gene (rep) of begomovirus causing yellow mosaic disease on soybean in Central Indian region is characterized. A total of 85 complete rep gene sequences of legume begomoviruses including sequence reported in this study were employed to delineate genetic diversity, population selection and evolutionary lineage. Nucleotide diversity analysis revealed that the major legume yellow mosaic viruses (LYMVs) viz., MYMV and MYMIV are less diverse than legume begomovirus population as a whole. Test of neutral evolution also reiterates the operation of purifying selection and population expansion of major legume begomoviruses. However interestingly, LYMVs as a whole, show decrease in population size and act of balancing or neutral selection. Recombinants have also been detected only among the isolates of MYMIV suggesting frequent genetic exchanges.Not Availabl